Multiple platform build/check report for BioC 3.6 - CHECK report for flowWorkspace on tokay1

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### Running command:
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###   rm -rf flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && mkdir flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.26.9.tar.gz >flowWorkspace.Rcheck\00install.out 2>&1 && cp flowWorkspace.Rcheck\00install.out flowWorkspace-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowWorkspace.buildbin-libdir --install="check:flowWorkspace-install.out" --force-multiarch --no-vignettes --timings flowWorkspace_3.26.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '3.26.9'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'flowWorkspace' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcT897F/R.INSTALL14c0e5a1850/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: missing file link 'estimateLogicle'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    lib    2.9Mb
    libs   6.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' values for
  'BH' 'cytolib'
are only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'RBGL' 'grDevices' 'graphics'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'flowCore:::.estimateLogicle' 'flowCore:::checkClass'
  'flowCore:::copyFlowSet' 'flowCore:::guid'
  'flowCore:::logicle_transform' 'graph:::.makeEdgeKeys'
  'lattice:::updateList' 'ncdfFlow:::.isValidSamples'
  'stats:::.splinefun'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
  partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for 'is'
.addGatingHierarchies : <anonymous>: no visible global function
  definition for 'tolower<-'
.computeCV : <anonymous>: no visible binding for global variable
  'xml.count'
.computeCV : <anonymous>: no visible binding for global variable
  'openCyto.count'
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for 'IQR'
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
.computeCV_gh : <anonymous>: no visible global function definition for
  'IQR'
.computeCV_gh : <anonymous>: no visible global function definition for
  'median'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable 'max_val'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable 'decade'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable 'offset'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable 'min_val'
.convertTrans : <anonymous>: multiple local function definitions for
  'f' with different formal arguments
.dropRedundantNodes : <anonymous>: no visible global function
  definition for 'is'
.getSingleCellExpression: no visible binding for global variable
  'parallel'
.graph_handler : asGraphNEL: no visible global function definition for
  'new'
.graph_handler : asGraphNEL: no visible global function definition for
  'validObject'
.load_gs: no visible global function definition for 'new'
.load_gs: no visible global function definition for '.hasSlot'
.load_gs: no visible global function definition for 'slot'
.mergeGates : <anonymous>: no visible global function definition for
  'extends'
.parse.pData: no visible binding for global variable '.'
.plotGate: no visible global function definition for 'new'
.plotGate: no visible global function definition for 'as.formula'
.preplot: no visible global function definition for 'as'
.preprocessMap: no visible binding for global variable 'old'
.preprocessMap: no visible binding for global variable '.'
.preprocessor: no visible binding for global variable 'groupName'
GatingSetList: no visible global function definition for 'as'
GatingSetList: no visible global function definition for 'validObject'
booleanFilter: no visible global function definition for 'new'
char2booleanFilter: no visible global function definition for 'new'
dropRedundantNodes : <anonymous>: no visible global function definition
  for 'is'
flowWorkspace.par.init: no visible global function definition for
  'gray'
getMergedStats: no visible binding for global variable 'sampleName'
mkformula: no visible global function definition for 'as.formula'
save_gslist: no visible binding for global variable 'slot'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
GatingSet,GatingHierarchy-character: no visible global function
  definition for 'new'
GatingSet,character-character: no visible global function definition
  for 'new'
GatingSet,flowSet-ANY: no visible global function definition for 'new'
Rm,character-GatingSetList-character: no visible global function
  definition for 'selectMethod'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSetList-ANY: no visible global function definition for
  'callNextMethod'
[,GatingSetList-ANY: no visible global function definition for 'as'
[[,GatingSet-character: no visible global function definition for 'new'
add,GatingHierarchy-logicalFilterResult: no visible global function
  definition for 'selectMethod'
add,GatingSet-filtersList: no visible global function definition for
  'selectMethod'
add,GatingSet-list: no visible global function definition for
  'selectMethod'
add,GatingSetList-filter: no visible global function definition for
  'selectMethod'
add,GatingSetList-filterList: no visible global function definition for
  'selectMethod'
add,GatingSetList-filters: no visible global function definition for
  'selectMethod'
add,GatingSetList-filtersList: no visible global function definition
  for 'selectMethod'
add,GatingSetList-list: no visible global function definition for
  'selectMethod'
getPopStats,GatingHierarchy: no visible binding for global variable
  'node'
keyword,GatingSetList-character: no visible global function definition
  for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
  for 'selectMethod'
openWorkspace,character: no visible global function definition for
  'new'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'as'
plotGate,GatingSetList-character: no visible global function definition
  for 'selectMethod'
rbind2,GatingSetList-missing: no visible global function definition for
  'new'
rbind2,GatingSetList-missing: no visible binding for global variable
  'slot'
recompute,GatingSetList: no visible global function definition for
  'selectMethod'
show,flowJoWorkspace: no visible global function definition for '.'
show,flowJoWorkspace: no visible binding for global variable
  'groupName'
transform,GatingSet: no visible global function definition for 'is'
Undefined global functions or variables:
  . .hasSlot IQR as as.formula callNextMethod decade extends gray
  groupName is max_val median min_val new node offset old
  openCyto.count parallel sampleName selectMethod slot tolower<-
  validObject xml.count
Consider adding
  importFrom("grDevices", "gray")
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "slot", "validObject")
  importFrom("stats", "IQR", "as.formula", "median", "offset")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
GatingHierarchy-class 3.26   0.13    6.72
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c flowJoWorkspace.cpp -o flowJoWorkspace.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<GatingSet>, std::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned j = 0; j < pops.size(); ++j){
                           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:562:27: warning: "/*" within comment [-Wcomment]
  * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
 ^
winFlowJoWorkspace.cpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
winFlowJoWorkspace.cpp:113:11: warning: unused variable 'minRange' [-Wunused-variable]
    double minRange=atof(transNode.getProperty("minRange").c_str());
           ^
In file included from C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:10,
                 from winFlowJoWorkspace.cpp:8:
C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp:440:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
winFlowJoWorkspace.cpp:539:7: note: 'quad' was declared here
  QUAD quad;
       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c workspace.cpp -o workspace.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ws2gh.cpp -o ws2gh.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ws2gs.cpp -o ws2gs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c wsNode.cpp -o wsNode.o
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o C:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'flowWorkspace'
    finding HTML links ... done
    GatingHierarchy-class                   html  
    GatingSet-class                         html  
    GatingSet-methods                       html  
    finding level-2 HTML links ... done

    GatingSetList-class                     html  
    add                                     html  
    asinh_Gml2                              html  
    asinhtGml2_trans                        html  
    booleanFilter-class                     html  
    checkRedundantNodes                     html  
    clone                                   html  
    compensate                              html  
    dropRedundantChannels                   html  
    dropRedundantNodes                      html  
    estimateLogicle.GatingHierarchy         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcT897F/R.INSTALL14c0e5a1850/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: missing file link 'estimateLogicle'
    filterObject                            html  
    flowData                                html  
    flowJo.fasinh                           html  
    flowJoTrans                             html  
    flowJoWorkspace-class                   html  
    flowJo_biexp_trans                      html  
    flowJo_fasinh_trans                     html  
    flowWorkspace-package                   html  
    flowWorkspace.par.get                   html  
    flowWorkspace.par.init                  html  
    flow_breaks                             html  
    flow_trans                              html  
    getCompensationMatrices                 html  
    getData-methods                         html  
    getFJWSubsetIndices                     html  
    getGate                                 html  
    getIndiceMat                            html  
    getIndices-GatingSet-name-method        html  
    getIndices                              html  
    getKeywords                             html  
    getMergedStats                          html  
    getNodes                                html  
    getParent                               html  
    getPopStats                             html  
    getSampleGroups                         html  
    getSamples                              html  
    getSingleCellExpression                 html  
    getTransformations                      html  
    groupByChannels                         html  
    groupByTree                             html  
    insertGate                              html  
    isNcdf                                  html  
    keyword                                 html  
    lapply-methods                          html  
    length                                  html  
    logicleGml2_trans                       html  
    logicle_trans                           html  
    loglevel                                html  
    markernames                             html  
    mkformula                               html  
    moveNode                                html  
    ncFlowSet-methods                       html  
    openWorkspace                           html  
    pData-methods                           html  
    parseWorkspace                          html  
    plot-methods                            html  
    plotGate-methods                        html  
    plotPopCV                               html  
    prettyAxis                              html  
    recompute                               html  
    sampleNames                             html  
    save_gs                                 html  
    set.count.xml                           html  
    setGate                                 html  
    setNode-methods                         html  
    standardize-GatingSet                   html  
    subset                                  html  
    transform                               html  
    transformerList                         html  
    updateChannels                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c flowJoWorkspace.cpp -o flowJoWorkspace.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:562:27: warning: "/*" within comment [-Wcomment]
  * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
 ^
winFlowJoWorkspace.cpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
winFlowJoWorkspace.cpp:113:11: warning: unused variable 'minRange' [-Wunused-variable]
    double minRange=atof(transNode.getProperty("minRange").c_str());
           ^
In file included from C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:10,
                 from winFlowJoWorkspace.cpp:8:
C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include/cytolib/gate.hpp:440:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
winFlowJoWorkspace.cpp:539:7: note: 'quad' was declared here
  QUAD quad;
       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c workspace.cpp -o workspace.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ws2gh.cpp -o ws2gh.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c ws2gs.cpp -o ws2gs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -IC:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c wsNode.cpp -o wsNode.o
mkdir -p "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o flowJoWorkspace.o getSingleCellExpression.o macFlowJoWorkspace.o setCounts.o winFlowJoWorkspace.o workspace.o ws2gh.o ws2gs.o wsNode.o C:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.26.9.zip
* DONE (flowWorkspace)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for flowWorkspace on tokay1

Summary

Command output

Installation output

Tests output

Example timings